Annotated VCF not correctly read in

[wyoungj]

Hi there.
I have downloaded the latest version (V4.14.1)
When using an annotated VCF (annotated using TabANNO) to specifiy variants to include in grouping, it results in an error:

FATAL ERROR -
No p value available for calculating Genomic Control. Check if markers were filtered!

This is despite using no HWE/callrate/hitscutoff filter.

Creating a groupfile myself does work however. Thus i presume it must be an issue with handling the annotated VCF?

I would be grateful for some help / not sure if this is a new bug...

The head of my annotated VCF
#CHROM POS ID REF ALT QUAL FILTER INFO
21 35819014 35819014 G A . . ALT_AF=;;ANNO=Utr3:KCNE1;ANNOFULL=KCNE1/NM_001127670:-:Utr3:Exon|KCNE1/NM_000219:-:Utr3:Exon|KCNE1/NM_001127669:-:Utr3:Exon|KCNE1/NM_001127668:-:Utr3:Exon;ONTARGET=
21 35819063 35819063 T C . . ALT_AF=;;ANNO=Utr3:KCNE1;ANNOFULL=KCNE1/NM_001127670:-:Utr3:Exon|KCNE1/NM_000219:-:Utr3:Exon|KCNE1/NM_001127669:-:Utr3:Exon|KCNE1/NM_001127668:-:Utr3:Exon;ONTARGET=
21 35819082 35819082 T C . . ALT_AF=;;ANNO=Utr3:KCNE1;ANNOFULL=KCNE1/NM_001127670:-:Utr3:Exon|KCNE1/NM_000219:-:Utr3:Exon|KCNE1/NM_001127669:-:Utr3:Exon|KCNE1/NM_001127668:-:Utr3:Exon;ONTARGET=

BW

Will

[abought]

Greetings,

Without excluding the possibility of other issues, as a first question, can you double check the version you are using? The current newest release is actually 4.15.1.

The 4.14.x versions had a few known calculations issues, including that development preview versions (labeled 4.14.1) were known to have issues with variant filtering/selection.

Also, the command reference documentation suggests that certain options may have defaults even if not explicitly specified. Do any of these apply to your use case?

[wyoungj]

Thanks for the reply.

Sorry, I meant version 4.15.1. (the one released only a few days ago)

None of the defaults apply to this case - Particularly as specifying the groupFile works where as annotatedVCF does not.

I would be grateful for any additional thoughts.

[abought]

Thanks for clarifying. It may take a bit of time to follow up (due to other tasks currently in flight)- I'll make a note to do so, and please let us know if you find anything first.

There have been other issues recently with handling of supporting files, so these reports are helpful.